MCP Server Design

mcp-server-design

Design the surface an MCP (Model Context Protocol) server exposes to AI agents — which tools/resources/prompts exist, what they're named, what their schemas and descriptions say. This is the highest-leverage phase: most bad MCP servers fail here, not in code. The failure this skill fixes: 1:1 API-wrapped, over-tooled, under-described servers that tank agent tool-selection accuracy and burn context.

Facts below target MCP spec revision 2025-11-25 (current as of 2026-07-20).

When NOT to use

• Writing the server code with an SDK → mcp-server-implementation.
• Adding OAuth/tokens → mcp-server-auth. Threat modeling → mcp-server-security.
• Testing/evals → mcp-server-testing. Shipping/registry → mcp-server-deployment.
• Designing plain REST/GraphQL APIs for human developers — different consumer, different rules (verbose CRUD is fine there; it is the anti-pattern here).
• Choosing which existing MCP servers to install (consumer question, not design).

Workflow

1. Decide whether a server should exist

Build an MCP server when 2+ AI clients need autonomous access to the system, or a workflow is reused across sessions ("earns its keep on the third reuse"). One bespoke agent you fully control + a one-off task → direct tool/function integration is simpler. A single static value → a resource on an existing server, not a new one. Check https://github.com/modelcontextprotocol/servers and the MCP Registry first — don't rebuild what exists.

2. Derive tools from workflows, not endpoints

Work top-down from the user workflows the agent must complete; never bottom-up from the API surface. Each tool should complete an outcome, doing multi-step orchestration server-side:

• get_user + list_orders + get_status → one orders_track_latest(email)
• list_users + list_events + create_event → calendar_schedule_event(...)
• read_logs (dump) → logs_search(query) returning matched lines + context

1:1 REST/OpenAPI auto-wrapping is the most-documented MCP anti-pattern: it multiplies round-trips, tokens, and hallucinated parameters. If a workflow needs ~5 chained tool calls, collapse it into one tool.

3. Enforce a tool budget

Tool definitions are injected into the model's context every turn (~350 tokens/tool) and selection accuracy degrades as the catalog grows — production teams converge on 5–15 tools per server (heuristic, not spec law; weaker models degrade earlier). Real fixes went 40→13 tools (GitHub Copilot) and 3 rebuilds→2 tools (Block's Linear server). Need more? Split by domain, permission level (read vs write), or performance profile — never by API resource. Run scripts/lint_tool_surface.py (below) to gate the count and names.

4. Assign each capability to the right primitive

Control-model test — who decides when it happens?

Don't cram workflow instructions into tool descriptions when a prompt is the right home, and don't model pure reference data as a parameterless tool without considering a resource first.

5. Name tools per current spec guidance

{service}_{action}_{resource} in snake_case: slack_send_message, tickets_search, sentry_get_error_details. Spec (SEP-986, 2025-11-25): 1–128 chars, case-sensitive, only A-Za-z0-9_-., unique per server. The service prefix prevents collisions when several servers are active. Verb-first actions; no spaces/brackets (some clients won't surface the tool at all).

6. Write descriptions as prompts, schemas as contracts

The description is what the model routes on — write it like onboarding docs for a new hire, not API docs. State: what it does (one specific sentence), when to use / when NOT to use, each parameter's exact format, and the return shape. "Gets commits" is a real production description and it is useless.

Schemas are validated contracts, not hints: flat, typed, top-level parameters with enums for constrained values, defaults, and unambiguous names (user_id, never user or a nested filters: dict the model must guess). Constraints belong in the schema (the protocol validates them), not in prose. Keep terminology identical across tools (user_id everywhere — never user_id here and accountId there).

7. Design responses for a context window

• Paginate every list: limit (default 20–50, capped), cursor/offset in, has_more + total_count out. Never dump unbounded records.
• response_format parameter ("concise" default / "detailed"): concise responses cut tokens ~2/3 in Anthropic's Slack example.
• Prefer human-readable identifiers (names alongside IDs) — resolving opaque UUIDs to names measurably reduces hallucinated follow-up parameters.
• Cap response size (~25k tokens is a common client-side cap) and tell the agent how to get the rest (offset/filter), don't truncate silently.

8. Write errors as recovery instructions

Tool errors are read by the model, not the user. Every failure message should say what went wrong and what to do next:

"Project 'proj_abc123' not found. Call projects_list to see valid IDs." "Rate limited. Retry after 30 seconds."

not Error 500 / raw tracebacks. (Wire-level mechanics — isError vs protocol errors — live in mcp-server-implementation.)

9. Declare honest annotations and gate destructive tools

Annotate behavior: readOnlyHint, destructiveHint, idempotentHint, openWorldHint (+ title). Clients drive confirmation UX from these — a lying annotation is a security bug. Make reads easy and writes expensive: destructive tools get explicit confirmation flows. (Full threat model: mcp-server-security.)

10. Lint the surface

python3 "${CLAUDE_SKILL_DIR}/scripts/lint_tool_surface.py" tools.json

Checks names (spec regex + snake_case + shared prefix), tool count, description quality floors, schema flatness/enums. Non-zero exit = fix before implementing.

Output spec

A design document (or direct edits) containing: the build/no-build decision with reasoning; a tool table (name, one-line outcome, annotations); primitive assignments with justification; per-tool description + flat typed schema + pagination/response_format for list tools; error-message examples; open questions for evaluation. Hand off to mcp-server-implementation to code it.

Gotchas

• Tool budget numbers are heuristics, not spec — the direction (fewer, higher-signal tools) is strongly corroborated; exact cliffs vary by model.
• "GET→resource, POST→tool" is wrong often enough to mislead — ask "is the model fetching context, or doing work?" instead.
• Resources/prompts have uneven client support; a design that depends on them must name its target clients or fall back to tools.
• Don't design around a single model: schemas that only a frontier model can navigate fail on the weakest client that connects.
• A 2026-07-28 spec revision (release candidate at authoring time) reshapes transports/lifecycle but does not change these surface-design rules; verify naming guidance at https://modelcontextprotocol.io/specification if months have passed.

Pointers

• references/tool-design.md — worked examples (bad→good descriptions and schemas), the annotations table, pagination/response contracts, token-cost numbers with sources, primitive decision tree, advanced patterns (HATEOAS navigator, progressive tool discovery).
• scripts/lint_tool_surface.py — deterministic surface gate (stdlib-only).